smithery/pwwang

1

cdr3clustering Cluster TCR/BCR clones by CDR3 sequences using GIANA or ClusTCR (both Faiss-based). Adds `CDR3_Cluster` column to met…

smithery/pwwang

0

2

cellcellcommunication Infer ligand-receptor interactions and cell-cell communication networks from single-cell RNA-seq data using the LIANA…

smithery/pwwang

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3

cellcellcommunicationplots Visualize cell-cell communication inference results from CellCellCommunication process. Creates publication-ready net…

smithery/pwwang

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4

clustermarkers Finds differentially expressed genes (markers) for clusters of T/B cells using Seurat's FindMarkers function.

smithery/pwwang

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5

clustermarkersofallcells Finds marker genes for clusters of ALL cells before T/B cell selection. This process identifies differentially expres…

smithery/pwwang

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6

loadingrnafromseurat Load pre-existing Seurat objects into the immunopipe pipeline instead of starting from raw count matrices via SampleI…

smithery/pwwang

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7

markersfinder Flexible marker finding process that wraps Seurat's FindMarkers function for custom group comparisons beyond simple c…

smithery/pwwang

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8

metabolicfeatures Performs enrichment analysis (GSEA-based) for metabolic pathways across different cell groups to identify significant…

smithery/pwwang

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9

modulescorecalculator Configuration skill for immunopipe process

smithery/pwwang

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10

sampleinfo The SampleInfo process is the pipeline entry point that reads sample metadata files, performs statistical analyses, a…

smithery/pwwang

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11

scfgsea Performs fast Gene Set Enrichment Analysis (GSEA) on single-cell data using fgsea R package.

smithery/pwwang

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12

scrnametaboliclandscape Comprehensive metabolic landscape analysis pipeline for scRNA-seq data.

smithery/pwwang

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13

seuratclusteringofallcells Performs coarse clustering on ALL cells (including T cells, B cells, and non-T/B cells) before cell type selection.

smithery/pwwang

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14

seuratclusterstats Generates comprehensive cluster statistics and visualizations for Seurat objects, including dimension reduction plots…

smithery/pwwang

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15

tessa TESSA (TCR and Expression Joint Clustering) is a Bayesian model that integrates T-cell receptor (TCR) sequence profil…

smithery/pwwang

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16

topexpressinggenes Identifies and visualizes the top expressing genes per cluster in T/B cells, followed by pathway enrichment analysis.…

smithery/pwwang

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17

topexpressinggenesofallcells Identifies and visualizes the top expressing genes per cluster across ALL cells (before T/B cell selection), followed…

smithery/pwwang

0